BL_Tier1.md
... ...
@@ -0,0 +1,36 @@
1
+### *32 total*
2
+
3
+|Gene|Summary| First BL study | Other entities | QC result |
4
+|:-:|:--:|:-:|:-|:-|
5
+|[ARID1A](ARID1A)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@barisicARID1AOrchestratesSWI2024]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@krysiakRecurrentSomaticMutations2017; @rossiCodingGenomeSplenic2012; @wienandGenomicAnalysesFlowsorted2019; @zhangGeneticHeterogeneityDiffuse2013]||
6
+|[BACH2](BACH2)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|||
7
+|[BCL6](BCL6)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@masclePointMutationsBCL62003], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]|PASS|
8
+|[BCL7A](BCL7A)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], FE[@balinas-gaviraFrequentMutationsAminoterminal2020], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@krysiakRecurrentSomaticMutations2017; @morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015]||
9
+|[BMP7](BMP7)|Tier 1 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|||
10
+|[CCND3](CCND3)|Tier 1 GE[@richterRecurrentMutationID32012], FE[@schmitzBurkittLymphomaPathogenesis2012]|[Richter et al](papers/richterRecurrentMutationID32012)|[@deschGenotypingCirculatingTumor2020; @jalladesExomeSequencingIdentifies2017; @morinFrequentMutationHistonemodifying2011]||
11
+|[CHD8](CHD8)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|||
12
+|[CREBBP](CREBBP)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@dunsCharacterizationDLBCLPMBL2021; @parryWholeExomeSequencing2013; @pasqualucciInactivatingMutationsAcetyltransferase2011]|PASS|
13
+|[DDX3X](DDX3X)|Tier 1 GE[@schmitzBurkittLymphomaPathogenesis2012], FE[@gongSequentialInverseDysregulation2021]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@mottokIntegrativeGenomicAnalysis2019; @reddyGeneticFunctionalDrivers2017]||
14
+|[FBXO11](FBXO11)|Tier 1 GE[@richterRecurrentMutationID32012], FE[@duanFBXO11TargetsBCL62011]|[Richter et al](papers/richterRecurrentMutationID32012)|[@arthurGenomewideDiscoverySomatic2018; @parryWholeExomeSequencing2013]||
15
+|[FOXO1](FOXO1)|Tier 1 GE[@schmitzBurkittLymphomaPathogenesis2012], FE[@trinhAnalysisFOXO1Mutations]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@dunsCharacterizationDLBCLPMBL2021; @morinFrequentMutationHistonemodifying2011]||
16
+|[GNA13](GNA13)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@muppidiLossSignalingGa132014]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015]||
17
+|[GNAI2](GNAI2)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], FE[@muppidiLossSignalingGa132014]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@drevalGeneticSubdivisionsFollicular2023; @morinMutationalStructuralAnalysis2013]||
18
+|[HIST1H1E](HIST1H1E)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@krysiakRecurrentSomaticMutations2017; @lohrDiscoveryPrioritizationSomatic2012; @reichelFlowSortingExome2015]||
19
+|[HNRNPU](HNRNPU)|Tier 1 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@reddyGeneticFunctionalDrivers2017]||
20
+|[ID3](ID3)|Tier 1 GE[@richterRecurrentMutationID32012]|[Richter et al](papers/richterRecurrentMutationID32012)|[@schmitzGeneticsPathogenesisDiffuse2018; @spinaGeneticsNodalMarginal2016]||
21
+|[KMT2D](KMT2D)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], FE[@zhangDisruptionKMT2DPerturbs2015]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@beaLandscapeSomaticMutations2013; @deschGenotypingCirculatingTumor2020; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012]||
22
+|[MYC](MYC)|Tier 1 GE[@johnstonCmycHypermutationBurkitt1992], FE[@freieGermlinePointMutation2024], aSHM|[Johnston et al](papers/johnstonCmycHypermutationBurkitt1992)|[@dunsCharacterizationDLBCLPMBL2021; @jalladesExomeSequencingIdentifies2017; @pasqualucciHypermutationMultipleProtooncogenes2001]||
23
+|[P2RY8](P2RY8)|Tier 1 GE[@muppidiLossSignalingGa132014], FE[@muppidiLossSignalingGa132014]|[Muppidi et al](papers/muppidiLossSignalingGa132014)|[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012]||
24
+|[PCBP1](PCBP1)|Tier 1 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
25
+|[PHF6](PHF6)|Tier 1 GE[@thomasGeneticSubgroupsInform2023]|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|[@reddyGeneticFunctionalDrivers2017]||
26
+|[PTEN](PTEN)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@pfeiferPTENLossDefines2013]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@reddyGeneticFunctionalDrivers2017]||
27
+|[RFX7](RFX7)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], FE[@weberPiggyBacTransposonTools2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@arthurGenomewideDiscoverySomatic2018]||
28
+|[RHOA](RHOA)|Tier 1 GE[@richterRecurrentMutationID32012], FE[@ohayreInactivatingMutationsGNA132016]|[Richter et al](papers/richterRecurrentMutationID32012)|[@zhangGeneticHeterogeneityDiffuse2013]||
29
+|[SIN3A](SIN3A)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@chapuyMolecularSubtypesDiffuse2018; @rossiCodingGenomeSplenic2012]||
30
+|[SMARCA4](SMARCA4)|Tier 1 GE[@richterRecurrentMutationID32012], FE[@fernandoFunctionalCharacterizationSMARCA42020]|[Richter et al](papers/richterRecurrentMutationID32012)|[@krysiakRecurrentSomaticMutations2017; @nadeuGenomicEpigenomicInsights2020; @reddyGeneticFunctionalDrivers2017]||
31
+|[TCF3](TCF3)|Tier 1 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
32
+|[TCL1A](TCL1A)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@reddyGeneticFunctionalDrivers2017]||
33
+|[TFAP4](TFAP4)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|||
34
+|[TP53](TP53)|Tier 1 GE[@wildaInactivationARFMDM2p53Pathway2004], FE[@katoUnderstandingFunctionstructureFunctionmutation2003]|[Wilda et al](papers/wildaInactivationARFMDM2p53Pathway2004)|[@beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012; @tiacciPervasiveMutationsJAKSTAT2018]||
35
+|[USP7](USP7)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@arthurGenomewideDiscoverySomatic2018]||
36
+|[WNK1](WNK1)|Tier 1 GE[@thomasGeneticSubgroupsInform2023]|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|[@hubschmannMutationalMechanismsShaping2021; @jalladesExomeSequencingIdentifies2017]||
... ...
\ No newline at end of file
BL_Tier2.md
... ...
@@ -0,0 +1,76 @@
1
+### *72 total*
2
+
3
+|Gene|Summary| First BL study | Other entities | QC result |
4
+|:-:|:--:|:-:|:-|:-|
5
+|[ADAMTS5](ADAMTS5)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
6
+|[ADNP](ADNP)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
7
+|[AGO4](AGO4)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
8
+|[ARHGEF1](ARHGEF1)|Tier 2 GE[@muppidiLossSignalingGa132014]|[Muppidi et al](papers/muppidiLossSignalingGa132014)|||
9
+|[BCL2](BCL2)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022], aSHM|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|[@morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021; @tanakaFrequentIncidenceSomatic1992]||
10
+|[BTG1](BTG1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022], FE[@almasmoumFrequentLossBTG12021], aSHM|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021]||
11
+|[C16orf48](C16orf48)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
12
+|[CARD4](CARD4)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS|
13
+|[CCNF](CCNF)|Tier 2 GE[@abateDistinctViralMutational2015]|[Abate et al](papers/abateDistinctViralMutational2015)|[@zhangGeneticHeterogeneityDiffuse2013]||
14
+|[CD79A](CD79A)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|[@rossiCodingGenomeSplenic2012]||
15
+|[CD83](CD83)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@dunsCharacterizationDLBCLPMBL2021; @morinMutationalStructuralAnalysis2013; @russler-germainMutationsAssociatedProgression2023]|PASS|
16
+|[CDC73](CDC73)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@reddyGeneticFunctionalDrivers2017]|PASS|
17
+|[CDKN2A](CDKN2A)|Tier 2 GE[@grandeGenomewideDiscoverySomatic2019], FE[@kannengiesserFunctionalStructuralGenetic2009]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@morinMutationalStructuralAnalysis2013; @spinaGeneticsNodalMarginal2016]||
18
+|[CDKN2C](CDKN2C)|Tier 2 GE[@thomasGeneticSubgroupsInform2023]|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|||
19
+|[CHD4](CHD4)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
20
+|[CPXM2](CPXM2)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
21
+|[CXCR4](CXCR4)|Tier 2 GE[@paneaWholeGenomeLandscape2019], FE[@zmajkovicovaGenotypephenotypeCorrelationsWHIM2022], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@khodabakhshiRecurrentTargetsAberrant2012; @krysiakRecurrentSomaticMutations2017]|PASS|
22
+|[DHCR7](DHCR7)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
23
+|[E2F2](E2F2)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
24
+|[EBF1](EBF1)|Tier 2 GE[@thomasGeneticSubgroupsInform2023], FE[@ramirez-komoSpontaneousLossLineage2017], aSHM|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|[@bohleRoleEarlyBcell2013; @drevalGeneticSubdivisionsFollicular2023; @reichelFlowSortingExome2015]||
25
+|[EDNRB](EDNRB)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
26
+|[EHD1](EHD1)|Tier 2 GE[@thomasGeneticSubgroupsInform2023]|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|||
27
+|[EIF4A1](EIF4A1)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|||
28
+|[ELP2](ELP2)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
29
+|[EPPK1](EPPK1)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|||
30
+|[ERAP1](ERAP1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
31
+|[EXOSC6](EXOSC6)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
32
+|[EZH2](EZH2)|Tier 2 GE[@loveGeneticLandscapeMutations2012], FE[@sneeringerCoordinatedActivitiesWildtype2010]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@morinSomaticMutationsAltering2010; @mottokIntegrativeGenomicAnalysis2019]|PASS|
33
+|[FLYWCH1](FLYWCH1)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
34
+|[GGTLA4](GGTLA4)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS|
35
+|[GTSE1](GTSE1)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
36
+|[HIST1H3D](HIST1H3D)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||PASS|
37
+|[HIST1H3I](HIST1H3I)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@krysiakRecurrentSomaticMutations2017]|PASS|
38
+|[HIST1H4J](HIST1H4J)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@mottokIntegrativeGenomicAnalysis2019]|PASS|
39
+|[HLA-DQB1](HLA-DQB1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
40
+|[IGLL5](IGLL5)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@chapuyMolecularSubtypesDiffuse2018; @deschGenotypingCirculatingTumor2020; @russler-germainMutationsAssociatedProgression2023]|PASS|
41
+|[IKZF3](IKZF3)|Tier 2 GE[@paneaWholeGenomeLandscape2019], FE[@lazarianHotspotMutationTranscription2021]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011]|PASS|
42
+|[IRF8](IRF8)|Tier 2 GE[@paneaWholeGenomeLandscape2019], FE[@qiuIRF8mutantCellLymphoma2024], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011; @mottokIntegrativeGenomicAnalysis2019]|PASS|
43
+|[KANK2](KANK2)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
44
+|[KLHL26](KLHL26)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
45
+|[KMT2C](KMT2C)|Tier 2 GE[@zhouSporadicEndemicBurkitt2019]|[Zhou et al](papers/zhouSporadicEndemicBurkitt2019)|[@sarkozyMutationalLandscapeGray2021; @zhangGeneticHeterogeneityDiffuse2013; @zhangGenomicLandscapeMantle2014]||
46
+|[MCL1](MCL1)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@dunsCharacterizationDLBCLPMBL2021; @reddyGeneticFunctionalDrivers2017]|PASS|
47
+|[MIR142](MIR142)|Tier 2 GE[@grandeGenomewideDiscoverySomatic2019], FE[@trissalMIR142LossofFunctionMutations2018], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@kwanhianMicroRNA142Mutated202012]||
48
+|[MKI67](MKI67)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@russler-germainMutationsAssociatedProgression2023]||
49
+|[MYO18A](MYO18A)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
50
+|[NBEAL1](NBEAL1)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS|
51
+|[NCOR2](NCOR2)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@sarkozyMutationalLandscapeGray2021; @spinaGeneticsNodalMarginal2016]||
52
+|[NOA1](NOA1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
53
+|[P2RY2](P2RY2)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS|
54
+|[PDCD11](PDCD11)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
55
+|[PIM1](PIM1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022], FE[@kuoRolePIM1Ibrutinibresistant2016], aSHM|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|[@drevalGeneticSubdivisionsFollicular2023; @dunsCharacterizationDLBCLPMBL2021; @pasqualucciHypermutationMultipleProtooncogenes2001]||
56
+|[PLCG2](PLCG2)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@fanComprehensiveCharacterizationDriver2020]|PASS|
57
+|[PPP6R2](PPP6R2)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
58
+|[PREX1](PREX1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
59
+|[RANBP6](RANBP6)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS|
60
+|[REV3L](REV3L)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
61
+|[RNF144B](RNF144B)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||PASS|
62
+|[RPL10](RPL10)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
63
+|[S1PR2](S1PR2)|Tier 2 GE[@muppidiLossSignalingGa132014], FE[@muppidiLossSignalingGa132014], aSHM|[Muppidi et al](papers/muppidiLossSignalingGa132014)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]||
64
+|[SAL3](SAL3)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
65
+|[TET2](TET2)|Tier 2 GE[@thomasGeneticSubgroupsInform2023], FE[@asmarGenomewideProfilingIdentifies2013]|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|[@albuquerqueEnhancingKnowledgeDiscovery2017]||
66
+|[TOP2A](TOP2A)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
67
+|[TTN](TTN)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
68
+|[VWA7](VWA7)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
69
+|[WDR90](WDR90)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
70
+|[WHAMM](WHAMM)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
71
+|[WNK2](WNK2)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||PASS|
72
+|[YY1AP1](YY1AP1)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
73
+|[ZAN](ZAN)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
74
+|[ZBTB7A](ZBTB7A)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|[@reddyGeneticFunctionalDrivers2017]||
75
+|[ZFP36L1](ZFP36L1)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015]|PASS|
76
+|[ZNF85](ZNF85)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
BL_Tier3.md
... ...
@@ -0,0 +1,75 @@
1
+### *70 total*
2
+
3
+|Gene|Summary| First BL study | Other entities | QC result |
4
+|:-:|:--:|:-:|:-|:-|
5
+|[ACAD9](ACAD9)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
6
+|[ACE](ACE)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
7
+|[ALPK2](ALPK2)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
8
+|[ATP2C2](ATP2C2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
9
+|[BRAF](BRAF)|Tier 3 GE[@loveGeneticLandscapeMutations2012], FE[@wanMechanismActivationRAFERK2004]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@tiacciBRAFMutationsHairycell2011]|FAIL|
10
+|[BRD4](BRD4)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
11
+|[BTG2](BTG2)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]|FAIL|
12
+|[C6orf27](C6orf27)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
13
+|[CAD](CAD)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
14
+|[CCT6B](CCT6B)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
15
+|[CD79B](CD79B)|Tier 3 GE[@paneaWholeGenomeLandscape2019], FE[@davisChronicActiveBcellreceptor2010]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@davisChronicActiveBcellreceptor2010; @drevalGeneticSubdivisionsFollicular2023]|FAIL|
16
+|[CDH17](CDH17)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
17
+|[COL4A2](COL4A2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
18
+|[CTCF](CTCF)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
19
+|[CYB5D1](CYB5D1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
20
+|[CYP4F22](CYP4F22)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
21
+|[DLGAP1](DLGAP1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
22
+|[DNMT1](DNMT1)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
23
+|[DTX1](DTX1)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@gomezUltraDeepSequencingReveals2023; @rossiCodingGenomeSplenic2012; @zhangGeneticHeterogeneityDiffuse2013]|FAIL|
24
+|[EIF2C4](EIF2C4)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
25
+|[EML2](EML2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
26
+|[ENTPD3](ENTPD3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
27
+|[EPHB2](EPHB2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
28
+|[ETS1](ETS1)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011]|FAIL|
29
+|[FAM129B](FAM129B)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
30
+|[FGFR3](FGFR3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
31
+|[FTCD](FTCD)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
32
+|[FZD3](FZD3)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
33
+|[GRIK5](GRIK5)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
34
+|[HIST1H1C](HIST1H1C)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011]|FAIL|
35
+|[HIST1H2AG](HIST1H2AG)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@krysiakRecurrentSomaticMutations2017; @morinMutationalStructuralAnalysis2013; @rossiCodingGenomeSplenic2012]|FAIL|
36
+|[HIST1H2AM](HIST1H2AM)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@chapuyMolecularSubtypesDiffuse2018; @krysiakRecurrentSomaticMutations2017]|FAIL|
37
+|[HIST1H2BK](HIST1H2BK)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@rossiCodingGenomeSplenic2012; @zhangGeneticHeterogeneityDiffuse2013]|FAIL|
38
+|[HIST1H3H](HIST1H3H)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
39
+|[HIST1H3J](HIST1H3J)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
40
+|[ICK](ICK)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
41
+|[ITPR3](ITPR3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@tiacciPervasiveMutationsJAKSTAT2018]|FAIL|
42
+|[KCNK10](KCNK10)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
43
+|[KIFC3](KIFC3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
44
+|[MAP3K6](MAP3K6)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
45
+|[MME](MME)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
46
+|[MTOR](MTOR)|Tier 3 GE[@paneaWholeGenomeLandscape2019], FE[@grabinerDiverseArrayCancerassociated2014]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
47
+|[MYH10](MYH10)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
48
+|[NOTCH1](NOTCH1)|Tier 3 GE[@loveGeneticLandscapeMutations2012], FE[@ryanCellRegulomeLinks2017]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@beaLandscapeSomaticMutations2013; @pasqualucciAnalysisCodingGenome2011; @rossiCodingGenomeSplenic2012]|FAIL|
49
+|[NRXN2](NRXN2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
50
+|[PABPC4L](PABPC4L)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
51
+|[PC](PC)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
52
+|[PCDHA11](PCDHA11)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
53
+|[PDZRN3](PDZRN3)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
54
+|[PIK3R1](PIK3R1)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
55
+|[POLRMT](POLRMT)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
56
+|[POR](POR)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
57
+|[PRSS22](PRSS22)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
58
+|[PTPRN](PTPRN)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
59
+|[PXDNL](PXDNL)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
60
+|[RBP3](RBP3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@lohrDiscoveryPrioritizationSomatic2012]|FAIL|
61
+|[RET](RET)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@fanComprehensiveCharacterizationDriver2020]|FAIL|
62
+|[SALL3](SALL3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGenomicLandscapeMantle2014]|FAIL|
63
+|[SAPS2](SAPS2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
64
+|[SBF1](SBF1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
65
+|[SF3B1](SF3B1)|Tier 3 GE[@loveGeneticLandscapeMutations2012], FE[@cazzolaBiologicClinicalSignificance2013]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@reddyGeneticFunctionalDrivers2017]|FAIL|
66
+|[SHANK1](SHANK1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
67
+|[SLC29A2](SLC29A2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
68
+|[SNTB2](SNTB2)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
69
+|[SYNGAP1](SYNGAP1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
70
+|[TBC1D9B](TBC1D9B)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
71
+|[TIGD6](TIGD6)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
72
+|[TPST2](TPST2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
73
+|[WDR7](WDR7)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
74
+|[ZNF229](ZNF229)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
75
+
BL_test.md
... ...
@@ -0,0 +1,24 @@
1
+---
2
+title: 'BL genes'
3
+bibliography: 'morinlab.bib'
4
+csl: 'NLM.csl'
5
+link-citations: true
6
+---
7
+
8
+## Origins of BL genes
9
+
10
+![](BL_sankey-1.svg)
11
+
12
+## Tier 1 BL genes
13
+
14
+[[include:BL_Tier1.md]]
15
+
16
+## Tier 2 BL genes
17
+
18
+[[include:BL_Tier2.md]]
19
+
20
+## Tier 3 BL genes
21
+
22
+[[include:BL_Tier3.md]]
23
+
24
+# References